In addition to supporting our population of beneficial microbes in the colon, suppressing the harmful species (or an overall excess of bacteria in the small intestine) can be critical to recovering from autoimmune disease. While the Keystone Approach focuses primarily on addressing bacterial imbalances through diet and probiotics, in some cases it may be necessary to go further and pursue a short-term treatment with one or more natural antimicrobial compounds.
If you do decide to go down this path, it is important keep the treatment period short (typically one month) and to choose compounds that do the least damage possible to the beneficial species of gut bacteria. To that end, it is best to avoid broad-acting antimicrobials, such as grapefruit seed extract and oregano oil, and instead choose the most targeted and specific options.
When it comes to suppressing the microbes most often implicated in SIBO and autoimmunity, without decimating the overall microbiome, the best options are Lactoferrin, Allicin, and Berberine.
For further information about these supplements, see Chapter 3 of The Keystone Approach.